Comments (1)
According to https://academic.oup.com/bioinformatics/article/25/14/1754/225615, MQ > 20 is good enough:
In each batch, BWA loads the full BWA index into memory, generates the chromosomal coordinate for each occurrence, estimates the insert size distribution from read pairs with both ends mapped with mapping quality higher than 20, and then pairs them.
from bwa-mem2.
Related Issues (20)
- Tag New Release HOT 7
- Difference in mapping quality and alignment for bwa mem2 compared to bwa mem HOT 5
- Is bwa really haplotype aware in non-human?
- error while index building HOT 2
- BWA-MEM2-LISA crashed with code 139 HOT 3
- [Question] How to install bwa-mem2-lisa
- Problems creating index with bwa-mem2 HOT 1
- MacOS M2 chip support HOT 1
- Segmentation fault with valle-inclan dataset - bwa-mem2 2.2.1 avx512bw HOT 1
- bwa and bwa-mem2 relative indexing memory usage HOT 2
- Segmentation fault using bwa-mem2:2.2.1--hd03093a_5 HOT 7
- Add option to align multiple .fastq files at once? HOT 2
- Erroring during install
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- MAPQ of supplementary alignments is unreliable
- core dumped! HOT 1
- bwa-mem2 produces different alignment coordinates than original bwa mem HOT 2
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from bwa-mem2.